Methods and materials for killing hiv infected cells

ABSTRACT

This document provides methods and materials involved in killing HIV infected cells (e.g., CD4 T cells). For example, methods and materials for using one or more Bcl-2 inhibitors (e.g., ABT-199) alone or in combination with one or more agents capable of reactivating HIV (e.g., latency reversing agent) to kill HIV infected cells (e.g., CD4 T cells) are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Application Ser. No.62/149,873, filed on Apr. 20, 2015. The disclosure of the priorapplication is considered part of the disclosure of this application,and is incorporated in its entirety into this application.

BACKGROUND 1. Technical Field

This document relates to methods and materials involved in killing HIVinfected cells (e.g., CD4 T cells). For example, this document providesmethods and materials for using one or more Bcl-2 inhibitors (e.g.,ABT-199) alone or in combination with one or more agents capable ofreactivating HIV (e.g., latency reversing agent) to kill HIV infectedcells (e.g., CD4 T cells).

2. Background Information

HIV is a retrovirus that causes the acquired immunodeficiency syndrome(AIDS), which is a medical condition where progressive failure of theimmune system leads to life-threatening opportunistic infections. TheHIV infection, while treatable for long periods of time, remains alargely incurable infection. On the other hand, an HIV infection was“cured” in one patient, which involved using myeloablative chemotherapyand maximally suppressive antiretroviral therapy (ART), followed by bonemarrow transplantation (BMT; Hater et al., N. Engl. J. Med., 360:692-698(2009)).

SUMMARY

This document provides methods and materials involved in killing HIVinfected cells (e.g., CD4 T cells). For example, this document providesmethods and materials for using one or more Bcl-2 inhibitors (e.g.,ABT-199) alone or in combination with one or more agents capable ofreactivating HIV (e.g., latency reversing agent) to kill HIV infectedcells (e.g., CD4 T cells). As described herein, Bcl-2 inhibitors (e.g.,ABT-199) alone or in combination with one or more agents capable ofreactivating HIV (e.g., latency reversing agent) can be used to kill HIVinfected cells (e.g., CD4 T cells such as latently HIV infected CD4 Tcells or central memory CD4 T cells).

In general, one aspect of this document features a method for killingHIV infected cells within a human infected with HIV. The methodcomprises, or consist essentially of, (a) administering a Bcl-2inhibitor to the human, and (b) administering a latency reversing agentto the human. The cells can be CD4⁺ T cells. The Bcl-2 inhibitor can beABT-199. The latency reversing agent can be selected from the groupconsisting of an HDAC inhibitor, a phorbol ester, IL-2, and abromodomain inhibitor.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Other features and advantages of the invention will be apparent from thefollowing detailed description, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1. Casp8p41 binds the BH3 binding grooves of antiapoptotic Bcl-2family members. A, 293T cells transfected with HA-empty vector,HA-Casp8p41, or HA-Casp8p41EK were immunoprecipitated withanti-HA-conjugated beads or agarose conjugated antibody (control IgG orBcl-2) and immunoblotted as indicated. B, Binding of 12.5-200 nMGST-Bcl-2 to immobilized GST-Casp8p41 as assessed by SPR. C, KDs ofGST-Bcl-2, GST-Bcl-xL and GST-Mcl-1 binding to GST-Casp8p41. D, Multiplelow-mass molecular dynamics simulation-refined model of the Casp8p41activator domain (green) binding the human Bcl-2 BH3-binding groove. E,Binding of 800 nM GST-Bcl-2 or GST-Bcl-2 R146A to immobilized Casp8p41.F, KDs determined as in panel E. G, Binding of 200 nM GST-Casp8p41 orGST-Casp8p41 Val150Glu/Leu157Lys to immobilized GST-Bcl-2. H, KDsdetermined as in panel G. Bars in C, F, and H: mean±SD from 3independent experiments.

FIG. 2. T_(CM) are more resistant to cell death than T_(EM). A,Representative flow data demonstrating immunophenotyping gating strategyfor naïve, central memory, and effector memory CD4 T cell analysis (leftpanel); light scatter characterization of cell viability and LIVE/DEADstaining for cell viability and death (right panel). B, C, PBMCs from 3uninfected donors were treated overnight with agonistic anti-Fasantibody CH11, cycloheximide (CHX), etoposide (ETP), camptothecin (CPT),carbonyl cyanide 3-chlorophenylhydrazone (CCCP) or H₂O₂, cell death wasassessed by flow cytometry using light scatter (B) and LIVE/DEAD stains(C). D, T_(CM) and T_(EM) were isolated from two HIV-infected donors bymagnetic bead separation and gene expression measured by NGS. Depictedare differentially expressed genes associated with cell proliferationand cell death sorted by log 2 fold change. Cell proliferation genes areat the top of the figure and cell death genes below. E, Cytosolicextracts from T_(CM) and T_(EM) were assessed for expression ofprocaspase 8 (Casp8) and Bcl-2 by Western blot and densitometry.Representative of three experiments. F, PBMCs from 2 HIV-infectedpatients were assessed for intracellular Casp8p41 expression in T cellsubsets, using CD3-negative cells as the negative gating control. PBMCsfrom five HIV-infected patients were assessed for intracellular Casp8p41expression in CD4⁺ T cell subsets and in CD3 negative cells (G).Depicted is representative flow cytometry data showing the gatingstrategy to determine intracellular Casp8p41 expression in CD4⁺ T cellsubsets: Naïve (TN), Central Memory (TCM), Effectory Memory (TEM), andtotal CD4 T cells (H). CD3-cells, which are not infected by HIV and thusdo not express HIV protease, were used as negative gating controls. (I)Gene expression differences in TCM versus TEM were validated in aseparate publicly available dataset of 6 uninfected donors.

FIG. 3. Bcl-2 overexpression decreases Casp8p41- or HIV-induced celldeath while increasing viral replication. A, Parental Jurkat T cells orJurkat cells stably overexpressing Bcl-2 were transfected withGFP-Casp8p41 or vector control and assessed for cell death via TUNEL. B,Relative GFP-Casp8p41 expression in EGFP⁺ Jurkat and Jurkat/Bcl-2 cells.Cells infected with HIVIIIb or mock infected were assessed for viabilityby LIVE/DEAD stain (C), cell associated HIV DNA content (D), and HIV p24production in culture supernatant (F), at day 9 post infection. Bars,mean±SD from 3 independent experiments. (H, E) Parental Jurkat cells orJurkat-BCL-2 cells were transfected with GFP-Casp8p41 or GFP alone andassessed for active BAK expression in GFP positive cells, using aconformational specific antibody which detects only active BAK. Depictedare individual MFI of active BAK (H) and representative dot plots (E)from two independent experiments. (F) Parental Jurkat cells orJurkat-BCL-2 cells were infected with HIVIIIb or mock infected, andassessed for HIV p24 production in culture supernatant at day 9 postinfection. Depicted are mean (SD) values of three independentexperiments. (G) Parental Jurkat T cells or Jurkat T cells stablyoverexpressing BCL-2 (Jurkat-BCL-2) were transfected with GFP-Casp8p41or GFP alone and assessed for cell death via TUNEL.

FIG. 4. Bcl-2 overexpression decreases TUNEL positivity induced byCasp8p41. Depicted is representative flow data from 6 hourspost-transfection of parental Jurkat cells and Jurkat+Bcl-2 cellscomparing TUNEL positivity in EGFP or EGFP-Casp8p41 expressing cells.Numbers depict the percent of GFP positive cells that are TUNELpositive.

FIG. 5. Bcl-2 overexpression increases cell viability after in vitro HIVinfection. Depicted is representative flow data assessing cell viabilityusing LIVE/DEAD staining in parental Jurkat cells and Jurkat+Bcl-2cells. Numbers depict percent of viable cells.

FIG. 6. Casp8p41 activator peptide binding to Bcl-2 is reduced byArg146Ala substitution. A, Binding of 800 nM of GST-Bcl-2 or GST-Bcl-2Arg146Ala to immobilized Casp8p41 activator peptide as assessed by SPR.B, Dissociation constants of GST-Bcl-2 and GST-Bcl-2 R146A to Casp8p41activator peptide, from three independent experiments. (P<0.05).

FIG. 7. ABT-199 decreases infected cell survival, HIV replication, andcell associated HIV DNA during acute HIV infection in vitro. A, Jurkat Tcells pretreated with DMSO or ABT-199 were transfected withEGFP-Casp8p41 or vector control and assayed for cell death by TUNEL. B,Primary CD4 T cells from 7 uninfected donors were infected with HIVIIIbor mock infected, treated with ABT-199 or diluent, and assayed for cellviability. C, Primary CD4 T cells were stimulated withphytohemagglutinin in the presence of ABT-199 or control and assayed forproliferation by CFSE staining. D, E, at day 9 post infection, HIV p24concentrations in culture supernatant (D) and cell-associated HIV DNA(E), were measured. F, Primary CD4 T cells were transfected with an HIVLTR-luciferase reporter, treated with increasing concentrations ofABT-199, and stimulated with prostratin (1 μM). After overnightincubation, luciferase activities were measured. G-I, Primary CD4 Tcells infected with HIV in the presence or absence of ABT-263 (1 μM)were assayed for viability (G), supernatant p24 production (H), and cellassociated HIV-DNA (I). Bars: mean±SD of 4 (A) or 3 (other panels)independent experiments.

FIG. 8. ABT-199 increases Casp8p41-induced apoptosis. Depicted arerepresentative dot plots assessing apoptosis as measured by TUNELstaining in Jurkat cells transfected with EGFP or EGFP-Casp8p41 andtreated with diluent (DMSO) or increasing concentrations of ABT-199.Numbers depict the percent of EGFP positive (or total for No DNA) cellsthat are TUNEL positive.

FIG. 9. ABT-199 decreases cell viability following acute HIV infectionin vitro. Depicted is representative flow data assessing cell viabilityusing LIVE/DEAD staining in primary CD4 T cells mock infected or HIVinfected and treated with DMSO or ABT-199 at day 9 post-infection.Numbers depict the percent of cells that are viable.

FIG. 10. Selective Bcl-2 inhibition reduces HIV DNA associated withcells after viral reactivation ex vivo. A, Primary CD4 T cells isolatedby negative selection from cryopreserved PBMCs of long-termvirologically suppressed HIV-infected patients (N=4) were treated for 16hours with ABT-199 or vehicle control in the presence of tenofovir andraltegravir, then exposed to plate bound aCD3 and soluble aCD28 antibodyto induce HIV reactivation. After 72 hour, cell associated HIV DNA wasmeasured. B, Freshly obtained peripheral CD4 T cells from an additional16 suppressed HIV-infected patients were treated with ABT-199 or DMSOfollowed by αCD3/αCD28 for 72 hours before cell associated HIV DNA wasmeasured. Depicted is the ratio of HIV DNA in ABT-199 treated vs.diluent treated samples for each patient with measurable HIV DNA in thediluent sample (n=11). C, Primary CD4 T cells from HIV-infected subjectswere treated with ABT-199 or diluent and assayed for intracellularCasp8p41 and active caspase 3 in the T_(C)M subset. Representative dataof three independent subjects. (D) Primary CD4 T cells from fourHIV-infected subjects were treated with venetoclax or diluent andinduced to reactivate HIV using CD3/CD28, and cell death measured in HIVP24 positive or negative cells using activated caspase 3 staining. (E)HIV RNA was measured in cell culture supernatant from 6 of the 11patient experiments from FIG. 10B.

FIG. 11. Venetoclax increases Casp8p41-induced apoptosis but sparescells that do not express Casp8p41. (A) Jurkat T cells pretreated withincreasing concentrations of venetoclax or diluent DMSO were transfectedwith EGFP-Casp8p41, vector control, or no DNA, and assayed for celldeath by TUNEL. Data are representative of three independentexperiments. (B) Primary CD4 T cells from seven uninfected donors weretreated with venetoclax (1 μM) or diluent, and assayed for cellviability by flow cytometry over 5 days. (C) Primary CD4 T cells fromfour uninfected donors were stimulated with phytohemagglutinin (2 μg/mL)in the presence of venetoclax (1 μM) or diluent and assayed forproliferation by CFSE staining. (D) Primary CD4 T cells from sevenART-suppressed HIV positive patients were treated with venetoclax (1 μM)or DMSO control for 24 hours and assessed for viability by trypan blueexclusion.

FIG. 12. Apoptotic cell death is associated with loss of protein andmRNA markers. Jurkat T cells stably expressing eGFP were treated withDMSO or CPT and assessed for cell viability by ATP content (A) and lightscatter (B) over time. (C) Expression of eGFP was measured by flowcytometry. (D) Actin mRNA expression was assessed by qRT-PCR andexpressed as mean Ct values normalized to baseline DMSO control. (E-G)Cell death was assessed by active-caspase 3 expression (E), TUNEL (F),and LIVE/DEAD viability stain (G) and compared between eGFP positive andeGFP negative cells. A-D values represent mean (range) of twoindependent experiments. E-G are representative of two independentexperiments.

FIG. 13. BCL-2 antagonism as a model of “prime, shock and kill” fordecreasing the HIV reservoir. (A) Reactivation of latent HIV does notlead to death of the reactivated cell due to inhibition of Casp8p41 bydirect binding to BCL-2. Therefore, the reactivated cell survives andproduces progeny virus. (B) Antagonism of BCL-2 activity (as withvenetoclax treatment) allows Casp8p41 to bind pro-apoptotic BAK, leadingto apoptotic death of the reactivated cell, and decreased total HIV DNA.

DETAILED DESCRIPTION

This document provides methods and materials for treating HIVinfections. For example, this document provides methods and materialsfor using one or more Bcl-2 inhibitors alone or in combination with oneor more other agents to treat HIV infections. In some cases, one or moreBcl-2 inhibitors can be used to cause latently HIV infected cells to diefollowing HIV reactivation in those latently HIV infected cells.

Any appropriate method can be used to identify a human having an HIVinfection. For example, HIV blood tests can be used to identify a humanhaving an HIV infection.

Once identified as having an HIV infection, the human can beadministered ART (e.g., maximally suppressive antiretroviral therapy) toprevent or reduce the level of repopulation of the HIV reservoir and oneor more Bcl-2 inhibitors to increase the susceptibility of latently HIVinfected cells to cell death upon HIV reactivation and/or to kill HIVreactivating cells.

An ART can include any appropriate anti-retroviral agent or combinationof anti-retroviral agents. Examples of anti-retroviral agents that canbe used for ART include, without limitation, HIV integrase inhibitors,HIV protease inhibitors, and reverse transcriptase inhibitors. Examplesof HIV integrase inhibitors include, without limitation, raltegravir(also known as Isentress or MK-0518), dolutegravir, and elvitegravir.Examples of HIV protease inhibitors include, without limitation,lopinavir and atazanavir. Examples of reverse transcriptase inhibitorsinclude, without limitation, emtricitabine, rilpivirine, and tenofovir.In some cases, combinations of anti-retroviral agents can be formulatedinto a single dosage form (e.g., a single pill or capsule) such asComplera® (emtricitabine, rilpivirine, and tenofovir), Atripla®(efavirenz, emtricitabine, and tenofovir DF), Stribild® (cobicistat,elvitegravir, emtricitabine, and tenofovir), and Triumeq® (abacavir,dolutegravir, and lamivudine).

Any appropriate Bcl-2 inhibitor or combination of Bcl-2 inhibitors(e.g., a combination of two, three, four, five, or more different Bcl-2inhibitors) can be used as described herein. Examples of Bcl-2inhibitors that can be used as described herein include, withoutlimitation, ABT-199, ABT263, and Sabutoclax.

In some cases, one or more agents that facilitate cell death by aCasp8p41 induced cell death pathway can be used in place of or incombination with one or more Bcl-2 inhibitors to treat HIV infections asdescribed herein. For example, one or more agents that facilitate celldeath by a Casp8p41 induced cell death pathway (e.g., SM164) can be usedalone to treat HIV infections. Agents that facilitate cell death by aCasp8p41 induced cell death pathway include those that can increasecaspase 8 polypeptide levels or can facilitate post mitochondrial deathsignaling. Examples of agents that can increase caspase 8 polypeptidelevels include, without limitation, those agents that can increasecaspase 8 polypeptide levels in CD4 T cells such as IL-2. Examples ofagents that can facilitate post mitochondrial death signaling include,without limitation, SMAC mimetics such as LBW242, SM164, and Birinapant.

In some cases, one or more Bcl-2 inhibitors can be formulated into apharmaceutically acceptable composition for administration to a humanhaving an HIV infection. For example, a therapeutically effective amountof ABT-199 can be formulated together with one or more pharmaceuticallyacceptable carriers (additives) and/or diluents. A pharmaceuticalcomposition can be formulated for administration in solid or liquid formincluding, without limitation, sterile solutions, suspensions,sustained-release formulations, tablets, capsules, pills, powders, andgranules. A pharmaceutical composition containing one or more Bcl-2inhibitors can be designed for oral or parenteral (includingsubcutaneous, intramuscular, intravenous, and intradermal)administration. When being administered orally, a pharmaceuticalcomposition containing one or more Bcl-2 inhibitors can be in the formof a pill, tablet, or capsule. Compositions suitable for parenteraladministration include aqueous and non-aqueous sterile injectionsolutions that can contain anti-oxidants, buffers, bacteriostats, andsolutes which render the formulation isotonic with the blood of theintended recipient; and aqueous and non-aqueous sterile suspensionswhich may include suspending agents and thickening agents. Theformulations can be presented in unit-dose or multi-dose containers, forexample, sealed ampules and vials, and may be stored in a freeze dried(lyophilized) condition requiring only the addition of the sterileliquid carrier, for example water for injections, immediately prior touse. Extemporaneous injection solutions and suspensions may be preparedfrom sterile powders, granules, and tablets.

In some cases, a pharmaceutically acceptable composition including oneor more Bcl-2 inhibitors can be administered systemically. For example,a composition containing a Bcl-2 inhibitor can be administeredsystemically orally or by injection to a human.

Effective doses can vary depending the route of administration, the ageand general health condition of the human, excipient usage, thepossibility of co-usage with other therapeutic treatments such as use ofanti-retroviral agents and/or latency reversing agents, and the judgmentof the treating physician.

An effective amount of a composition containing one or more Bcl-2inhibitors can be any amount that increases the susceptibility oflatently HIV infected cells to cell death upon HIV reactivation, therebycausing the latently HIV infected cells to die, without producingsignificant toxicity to the human. If a particular human fails torespond to a particular amount, then the amount of Bcl-2 inhibitor canbe increased by, for example, two fold. After receiving this higheramount, the human can be monitored for both responsiveness to thetreatment and toxicity symptoms, and adjustments made accordingly. Theeffective amount can remain constant or can be adjusted as a slidingscale or variable dose depending on the human's response to treatment.Various factors can influence the actual effective amount used for aparticular application. For example, the frequency of administration,duration of treatment, use of multiple treatment agents, route ofadministration, and severity of the HIV infection may require anincrease or decrease in the actual effective amount administered.

The frequency of administration of a composition containing one or moreBch 2 inhibitors can be any frequency that increases the susceptibilityof latently HIV infected cells to cell death upon HIV reactivation,thereby causing the latently HIV infected cells to die, withoutproducing significant toxicity to the human. For example, the frequencyof administration can be from about daily to about once a week. Thefrequency of administration can remain constant or can be variableduring the duration of treatment. As with the effective amount, variousfactors can influence the actual frequency of administration used for aparticular application. For example, the effective amount, duration oftreatment, use of multiple treatment agents, route of administration,and severity of the HIV infection may require an increase or decrease inadministration frequency.

An effective duration for administering a composition containing one ormore Bcl-2 inhibitors can be any duration that increases thesusceptibility of latently HIV infected cells to cell death upon HIVreactivation, thereby causing the latently HIV infected cells to die,without producing significant toxicity to the human. Thus, the effectiveduration can vary from several months to several years. In general, theeffective duration for the treatment of an HIV infection as describedherein can range in duration from about two months to about five years.Multiple factors can influence the actual effective duration used for aparticular treatment. For example, an effective duration can vary withthe frequency of administration, effective amount, use of multipletreatment agents, route of administration, and severity of the HIVinfection being treated.

In some cases, a human having an HIV infection can be treated with oneor more Bcl-2 inhibitors as described herein in combination with (a) oneor more anti-retroviral agents, (b) one or more latency reversingagents, (c) one or more immunotherapeutic agents, (d) one or morevaccines (e.g., a vaccine formulated for assisting in the treatment ofan HIV infection), (e) one or more nucleic acid-based therapies, (f) oneor more polypeptides designed to restrict HIV expression such as TRIMSalpha chimeric polypeptides, and (g) one or more advanced (e.g., thirdor later generation) chimeric antigen receptors expressed on CD8 T cellsor NK cells designed to generate anti-HIV immunity. Examples of latencyreversing agents that can be used in combination with one or more Bcl-2inhibitors as described herein include, without limitation, HDACinhibitors, phorbol esters, IL-2, bromodomain inhibitors, and thosedescribed elsewhere (Bullen et al., Nature Medicine, 20:425-429 (2014)).Examples of HDAC inhibitors that can be used as latency reversing agentsinclude, without limitation, vorinostat, panabinostat, and valproicacid. Examples of phorbol esters that can be used as latency reversingagents include, without limitation, prostratin and PMA. An example of abromodomain inhibitor that can be used as a latency reversing agentincludes, without limitation, JQ1 ((S)-tert-butyl2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetate).

Examples of immunotherapeutic agents that can be used in combinationwith one or more Bcl-2 inhibitors as described herein include, withoutlimitation, IL-15, CD4 immunotoxin, and neutralizing anti-HIVantibodies. For example, a human having an HIV infection can beadministered one or more Bcl-2 inhibitors as described herein and IL-15.

Examples of vaccines that can be used in combination with one or moreBcl-2 inhibitors as described herein include, without limitation, HIVtat or env antigens delivered by any number of platforms includinggenetic immunization, viral or virus like particle delivery, or deliveryas recombinant proteins. The HIV antigens can be delivered withadjuvants such as CPG or GM-CSF. In some cases, a human having an HIVinfection can be administered one or more Bcl-2 inhibitors as describedherein and a HIV tat or env vaccine.

Examples of nucleic acid-based therapies that can be used in combinationwith one or more Bcl-2 inhibitors as described herein include, withoutlimitation, nucleic acid molecules having the ability to reduce CCRSpolypeptide expression (e.g., siRNA molecules designed to reduce CCRSpolypeptide expression) and TALEN or CRISPR/Cas constructs designed toexcise HIV DNA. For example, a human having an HIV infection can beadministered one or more Bcl-2 inhibitors as described herein and ansiRNA molecule designed to reduce CCr5 polypeptide expression.

In some cases, a human having an HIV infection can be treated with oneor more Bcl-2 inhibitors as described herein in combination with one ormore anti-retroviral agents plus any one or more of (a) one or morelatency reversing agents, (b) one or more immunotherapeutic agents, (c)one or more vaccines (e.g., a vaccine formulated for assisting in thetreatment of an HIV infection), and (d) one or more nucleic acid-basedtherapies.

In some cases, the level of HIV infected cells within a human beingtreated can be monitored during the course of treatment. Any appropriatemethod can be used to determine the level of HIV infected cells within ahuman. For example, the level of HIV infected cells within a human canbe assessed using PCR based detection methods (nested or un-nested) fordetecting HIV DNA, quantitative viral outgrowth assays (QVOA) formeasuring replication competent HIV levels, or TILDA (Tat/rev; InducedLimiting Dilution Assay) that can measure the frequency of cells withmultiply spliced HIV RNA as a surrogate for replication competent HIV.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1—Bcl-2 Inhibition Facilitates Killing of HIV InfectedCells and Reduces Cell Associated HIV DNA Cell Culture

Jurkat cells and HEK 293T cells were obtained from American Type CultureCollection (Manassas, Va.). Jurkat/Bcl-2 cells were created bytransfecting Jurkat with a pcDNA-3 encoding Bcl-2 (obtained from Dr.Stan Korsmeyer), selecting for 30 days, and assessing Bcl-2 expressionby immunoblotting. HIV-uninfected PBMCs were harvested by ficollgradient centrifugation from Leukocyte Reduction System apheresischambers provided by healthy volunteer blood donors. Primary bulk CD4 Tcells were isolated using RosetteSep™ Human CD4⁺ T Cell EnrichmentCocktail (StemCell Technologies), activated for 24 hours with 1 μg/mLphytohemagglutinin, washed in medium, and incubated for 48 hours with 50units/mL IL-2 prior to HIV infection. TCM and TEM were treated withCH-11 anti-F as antibody (1 μg/mL), cycloheximide (CHX, 30 μM),etoposide (20 μM), camptothecin (20 μM), carbonyl cyanide3-chlorophenyl-hydrazone (CCCP, 1 μM), or H₂O₂ (0.35 mM) overnight toinduce cell death.

Plasmid and Peptide Preparation

Casp8p41 in pEGFP, pcDNA3, and pGEX-4T were described elsewhere (Nie etal., Open Virol. 1, 2:1-7 (2008); and Bren et al., PLoS One, 3:e2112(2008)). Plasmids encoding Bcl-2, Bcl-xL, and Mcl-1 were describedelsewhere (Smith et al., J. Biol. Chem., 286:17682-17692 (2011)). Theindicated Casp8p41 and BCL-2 mutations were introduced usingsite-directed mutagenesis (Agilent Technologies, Santa Clara, Calif.)and confirmed by sequencing. The Casp8p41 BH3-like peptide(DMNLLDIFIEMEKRVILGEGKLDILKRVCAQ; SEQ ID NO:1), N-terminal controlpeptide (MDFSRNLYDIGEQLDSEDLASLK; SEQ ID NO:2) and Bim BH3 peptide (Daiet al., J. Cell. Biol., 194:39-48 (2011)) were synthesized by solidphase synthesis.

Transfection

HEK 293T cells were transfected using Lipofectamine (Invitrogen,Carlsbad, Calif.) according to manufacturer's protocol. Jurkat cellswere transfected using a square wave electroporator (BXT, San Diego,Calif.) at 320 V.

Immunoprecipitation and Immunoblotting

293T cells transfected with empty vector, HA-Casp8p41, or HA-Casp8p41EKwere collected after 24 hours, washed with PBS, and lysed (20 mMTris/HCl pH 7.5, 150 mM NaCl, 1% CHAPS, 2 μg/mL aprotinin, 10 μg/mLleupeptin, 2 μg/mL pepstatin, and 1 mM PMSF) for 10 minutes on ice andcentrifuged at 15000 g for 5 minutes at 4° C. Aliquots containing 500 μgprotein were precleared with 25 μL Protein A/G-agarose (Santa CruzBiotechnology, Santa Cruz, Calif.), incubated with 5 μg anti-Bcl-2 cloneC22 (Santa Cruz Biotechnology, Santa Cruz, Calif.) overnight at 4° C.,supplemented with 10 μL Protein-A/G agarose. Beads were washed withlysis buffer 3 times in 10 fold the volume of the beads. Bound proteinwas eluted and subjected to SDS-PAGE followed by immunoblotting asdescribed elsewhere (Sainski et al., J. Virol., 85:7965-7975 (2011)).Primary antibodies used were: anti-HA peroxidase high affinity 3F10(Roche, St. Louis, Mo.) or anti-Bcl-2 clone C22, Mcl-1 clone 22, orBcl-xL clone s18 (Santa Cruz Biotechnology, Santa Cruz, Calif.).

Protein Expression and Purification

After plasmids encoding GST tagged proteins were transformed into E.coli BL21 or DH5α by heat shock, bacteria were grown to an opticaldensity of 0.8 and induced with 1 mM IPTG for 3 hours at 37° C. Bacteriawere disrupted by freezing and thawing in calcium- and magnesium-freeDulbecco's phosphate buffered saline (PBS) containing 0.1% Triton X-100,2 μg/mL aprotinin, 10 μg/mL leupeptin, 2 μg/mL pepstatin, and 1 mM PMSF,then sonicated three times for 15 sec/min on ice. GST-tagged proteinswere purified with glutathione-agarose (Thermo Fisher Scientific,Rockford, Ill.).

Surface Plasmon Resonance (SPR)

Proteins for SPR were further purified by FPLC on Superdex 5200,concentrated in a centrifugal concentrator (Centricon, Millipore),dialyzed against Biacore buffer (10 mM HEPES (pH 7.4), 150 mM NaCl, 0.05mM EDTA, and 0.005% (w/v) Polysorbate 20) and stored at 4° C. for <48hours before use. Binding assays were performed at 25° C. on a Biacore3000 biosensor after proteins were immobilized on a CMS chip (GEHealthcare). Ligands were injected at 30 μL/minute for 1 minute inBiacore buffer. Bound protein was allowed to dissociate in Biacorebuffer at 30 μL/minute for 10 minutes and then desorbed with 2 M MgCl₂.Binding kinetics were derived using BIA evaluation software (Biacore,Uppsala, Sweden).

Flow Cytometry

Immunophenotyping of T cell subsets was performed using multicolor flowcytometry with monoclonal antibodies to human CD3 (Alexa700, BDPharmingen), CD4 (FITC, BD Pharmingen), CD8 (Pacific Blue, BDPharmingen), CD27 (PE, BD Pharmingen), and CD45RO (ECD, BeckmanCoulter). Central memory T cells (T_(CM)) were defined asCD3⁺CD4⁺CD27⁺CD45RO⁺, and effector memory T cells (T_(EM)) were definedas CD3⁺CD4⁺CD27⁻CD45RO^(+/−) (Brenchley et al., J. Exp. Med.,200:749-759 (2004)). Intracellular expression of Casp8p41 was assessedas described elsewhere (Cummins et al., AIDS Res. Hum. Retroviruses,30:476-479 (2014)). Cell death was measured using LIVE/DEAD® FixableAqua dead cell stain (Invitrogen) or TUNEL (Roche) according tomanufacturers' protocols. Cell proliferation was measured using aCellTrace™ CFSE Cell Proliferation Kit (Life Technologies) according tomanufacturer's protocol. FACS analysis was performed on either a FACScanor LSRII flow cytometer (BD Biosciences) based on multiparameter needs.FACS data were analyzed using FlowJo software (Tree Star Inc).

HIV Infections

Jurkat and Jurkat/Bcl-2 cells were infected overnight, while primaryPHA-activated CD4 T cells were infected for 6 hours with HIV-1IIIb (NIHAIDS Reagent Program). Aliquots of the same infectious supernatant wereused for all experiments. Cells were then washed three times andincubated in fresh medium. At the indicated time points, HIV-1 p24 inthe cell culture supernatant was measured by RETROTEK™ ELISA kits(Zeptometrix Corporation) according to manufacturer's protocol. Cellassociated HIV-1 DNA was assayed using a modification of the protocoldescribed elsewhere (Liszewski et al., Methods, 47:254-260 (2009)).Briefly, total DNA was extracted using the Qiagen DNeasy Blood andTissue kit (Hilden, Germany) and analyzed by a real-time polymerasechain reaction (PCR) assay specific for HIV-LTR and β-globin. A standardcurve of pNL4-3 plasmid from 10⁶ through to 10 copies was used as aninternal control. 300 nM of the sense primer RU5-F5′-TTAAGCCTCAATAAAGCTTGCC-3′ (SEQ ID NO:3) and antisense primer RU5-R5′-GTTCGGGCGCCACTGCTAGA-3′ (SEQ ID NO:4) were used in conjunction with300 nM dual-labeled fluorogenic TaqMan probe5′-FAM-CCAGAGTCACACAACAGACGGGCACA-TAMRA-3′ (SEQ ID NO:5). For a 20 μLreaction, 10 μl of gene expression master mix (Applied Biosystems,Carlsbad, Calif.) was used with 5 μL of genomic DNA. PCR conditionsinvolved one cycle of 95° C. for 3 minutes followed by 45 cycles of 95°C. for 15 seconds and 60° C. for 1 minute. Total HIV-1 DNA was comparedand normalized with genomic DNA, determined by β-globin. HIV-1 proviralDNA levels were expressed as HIV-1 copies/β-globin genomic equivalent of10⁶ cells.

Next Generation Sequencing

Primary T_(CM) and T_(EM) were isolated using CD4⁺ Central Memory T CellIsolation and CD4⁺ Effector Memory T Cell Isolation Kits (MACS MiltenyiBiotec). After RNA was extracted (Qiagen RNA easy kit), the quality oftotal RNA samples was assessed by Agilent Bioanalyzer (Santa Clara,Calif.). RNA libraries were prepared according to the manufacturer'sinstructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego,Calif.). Poly-A mRNA was purified from total RNA using oligo dT magneticbeads. The purified mRNA was fragmented at 95° C. for 8 minutes, elutedfrom the beads, and primed for first strand cDNA synthesis. The RNAfragments were then copied into first strand cDNA using SuperScript IIIreverse transcriptase and random primers (Invitrogen, Carlsbad, Calif.).Second strand cDNA synthesis was performed using DNA polymerase I andRNase H. The double-stranded cDNA was purified using a single AMPure XPbead (Agencourt, Danvers, Mass.) clean-up step. cDNA ends were repairedand phosphorylated using Klenow, T4 polymerase, and T4 polynucleotidekinase followed by a single AMPure XP bead clean-up. The blunt-endedcDNAs were modified to include a single 3′ adenylate (A) residue usingKlenow exo-(3′ to 5′ exo minus). Paired-end DNA adaptors (Illumina) witha single “T” base overhang at the 3′ end were ligated to the ‘A tailed’cDNA population. Unique indexes, included in the standard TruSeq Kits(12-Set A and 12-Set B) were incorporated at the adaptor ligation stepfor multiplex sample loading on the flow cells. The resulting constructswere purified by two consecutive AMPure XP bead clean-up steps. Theadapter-modified DNA fragments were then enriched by 12 cycles of PCRusing primers included in the Illumina Sample Prep Kit. Libraries wereloaded onto paired end flow cells at concentrations of 8-10 pM togenerate cluster densities of 700,000/mm² following Illumina's standardprotocol using the Illumina cBot and cBot Paired end cluster kit version3. The flow cells were sequenced as 51×2 paired end reads on an IlluminaHiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12data collection software. Base-calling was performed using Illumina'sRTA version 1.17.21.3. Data were analyzed according to a Mayo Clinicdeveloped protocol for analyzing RNA-Sequencing data (see, e.g., theWorld Wide Web at “biomedcentral.com/content/pdf/1471-2105-15-224.pdf”).

Once the gene counts were provided by MAP-RSeq, a differentialexpression and gene set enrichment analysis was performed. DESeq33, an rpackage, was used to normalize and quantify log fold change, p-values,and the false discovery rate between the groups. A hypergeometric testwas then performed on all targets with an absolute log 2 fold change ofgreater than 1 to investigate enrichment of genes associated with celldeath and cell proliferation. Cell death and cell proliferation geneswere gathered from DeathBase (Diez et al., Cell Death Differ.,17:735-736 (2010), Gene Ontology (Ashburner et al., Nat. Genet.,25:25-29 (2000), and KEGG pathways (Kanehisa and Goto, Nucleic AcidsRes., 28:27-30 (2000)).

Statistical Analysis

Mean values of experimental results were compared by t-tests (non-pairedfor transformed cell line experiments, and paired for primary cellexperiments) or ANOVA or Friedman tests as appropriate. Results of timecourse experiments were compared by area under the curve analyses, withmean AUC values compared by t-tests. P<0.05 considered statisticallysignificant.

Molecular Modeling

The initial structure of the Casp8p41.Bcl-2 complex was generated bymanually docking the activator domain of Casp8p41 (residues 142-162) inthe a-helical conformation into the vacated BH3-binding groove of Bcl-2(residues 50-203) that was taken from the crystal structure of humanBcl-2 (Protein Data Bank ID: 4AQ3; residue 9 of the 4AQ3 structurecorresponds to residue 50 of the human Bcl-2 sequence of NCBI AccessionID of P10415). This manual docking placed V150^(Casp8p41) in theproximity of L137^(Bcl-2) and L157^(Casp8p41) close to V148^(Bcl-2). AllGlu, Asp, Arg, and Lys residues were treated as GLU, ASP, ARG, and LYS,respectively. His94^(Bcl-2) was treated as HIE, and all other Hisresidues were treated as HIP. The topology and coordinate files of thecomplex were generated by using LEAP of AmberTools 1.5 (University ofCalifornia, San Francisco). The complex was refined by energyminimization using SANDER of AMBER 11 (University of California, SanFrancisco) with a dielectric constant of 1.0 and 200 cycles ofsteepest-descent minimization followed by 300 cycles ofconjugate-gradient minimization using AMBER forcefield FF12MC. Developedby Yuan-Ping Pang, FF12MC is based on AMBER forcefield FF99 with changesof (i) reducing all atomic masses by tenfold to improve configurationalsampling (Pang, Biochem. Biophys. Res. Commun., 452: 588-592 (2014)),(ii) shortening C—H bonds by 10-14% (1.09 Å to 0.98 Å for the aliphatic;1.08 Å to 0.93 Å for the aromatic) (Pang, Biochem. Biophys. Res.Commun., 458:352-355 (2015)), and (iii) zeroing torsion potentialsinvolving a nonperipheral sp3 atom with reduction of the 1-4 interactionscaling factors of protein backbone torsions φ and ψ (from 2.00 to 1.00for the van der Waals interaction; from 1.20 to 1.18 for theelectrostatic interaction) (Pang, Biochem. Biophys. Res. Commun., 457:183-186 (2015)). The energy minimized complex was then solvated by usingthe LEAP module with 5946 TIP3P water molecules with the distanceparameter of 8.2 Å for the solvatebox command. The solvated complexsystem was energy-minimized for 100 cycles of steepest-descentminimization followed by 900 cycles of conjugate-gradient minimizationto remove close van der Waals contacts in the system, then heated from 0to 300 K at a rate of 10 K/ps under constant temperature and constantvolume, and finally simulated in ten unique, independent 10-ns moleculardynamics simulations using PMEMD of AMBER 11 with FF12MC. The ten uniqueseed numbers for initial velocities of Simulations 1-10 are 1804289383,846930886, 1681692777, 1714636915, 1957747793, 424238335, 719885386,1649760492, 596516649, and 1189641421, respectively. These all-atom,isothermal-isobaric MD simulations used (i) a dielectric constant of1.0, (ii) the Berendsen coupling algorithm (Berendsen et al., J. Chem.Phys., 81:3684-3690 (1984)), (iii) the Particle Mesh Ewald method tocalculate long-range electrostatic interactions (Darden et al., J. Chem.Phys., 98:10089-10092 (1993), (iv) a time step of 1.0 fs, (v)SHAKE-bond-length constraints applied to all the bonds involving the Hatom, (vi) a protocol to save the image closest to the middle of the“primary box” to the restart and trajectory files, (vii) a formattedrestart file, (viii) a nonbonded cutoff of 8.0 Å, and (ix) defaultvalues of all other inputs of PMEMD. All simulations were performed onten 12-core Apple Mac Pro microcomputers with Intel Westmere (2.40 GHz)processors. A cluster analysis of all conformations saved at 100-psintervals from the ten 10-ns MD simulations was performed using PTRAJ ofAmberTools 1.5 with the average-linkage algorithm (Shao et al., J. Chem.Theory Comput., 3:2312-2334 (2007)) (epsilon of 2.0 Å and root meansquare coordinate deviation on all Ca atoms of the BH3-like domain). Theoccurrences of the three most populated clusters are 67%, 6%, and 5%,respectively. The structure displayed in FIG. 1D is the representativeconformation of the most populated cluster identified by PTRAJ.

Results

During acute HIV infection, CD4 T cell death is initiated when viral RNAis detected by RIG-I (Solis et al., J. Virol., 85:1224-1236 (2011); andJiang et al., Nature 479, 423-427 (2011), reverse transcribed viral DNAis detected by IFI-16 (Doitsh et al., Nature, 505:509-514 (2014); andMonroe et al., Science, 343:428-432 (2014)), or HIV integrase-inducednicking of the host DNA is detected by DNA-PK (Cooper et al., Nature,498:376-379 (2013)). When these death mechanisms fail, HIV integratesinto the host genome and may enter a latent state in which the virus istranscriptionally silent, replication competent, and resistant tocurrent therapies or immune attack. Upon viral reactivation fromlatency, which occurs during T cell activation, these innate immunesensing mechanisms are not activated, but HIV protease-mediated cleavageof the host protein procaspase 8 (Nie et al., Cell Death Differ.,9:1172-1184 (2002); and Nie et al., Open Virol. J., 2:1-7 (2008))generates a fragment (Casp8p41) with an a-helical domain that directlyactivates the pro-apoptotic mitochondrial protein Bak to facilitateHIV-induced killing (Sainski et al., J. Cell. Biol., 207:159 (2014)).

As described herein, central memory CD4 T cells, the principal reservoirof HIV, are intrinsically resistant to cell death due, in part, toelevated expression of Bch 2. Further, it was demonstrate that Bcl-2binds Casp8p41, inhibits Casp8p41-mediated killing, and diminishes Tcell death following acute HIV infection in vitro, resulting inincreased HIV production. Conversely, antagonizing Bcl-2 selectivelypromoted death of Casp8p41-containing cells and diminished HIV DNAfollowing either acute HIV infection or HIV reactivation from latency exvivo. These results demonstrate that apoptosis sensitization followed byHIV reactivation can reduce HIV burden.

Once integrated into host DNA, HIV can remain in a latent state foryears. In patients on suppressive ART, T_(CM), which are long lived andproliferate in response to antigenic re-stimulation, constitute theprincipal HIV reservoir (Jaafoura et al., Nat. Commun., 5:5407 (2014)).By contrast, T_(EM) are a lesser reservoir (Chomont et al., Nat. Med.,15:893-900 (2009)) and have a shorter half-life (Macallan et al., J.Exp. Med., 200:255-260 (2004)). To assess whether the longer life spanof T_(CM) reflects intrinsic resistance to death stimuli, PBMCs fromuninfected donors were treated with proapoptotic stimuli. T_(CM) wereless susceptible than T_(EM) to Fas ligation and triggers of themitochondrial apoptotic pathway (FIG. 2A-2C). RNAseq performed on T_(CM)and T_(EM) revealed increased expression of six proliferation genes anddecreased expression of 46 cell death genes by at least 2-fold in T_(CM)(p=6.5×10⁻⁶ for enrichment of the death and proliferation gene sets,FIG. 2D), providing a potential explanation for the apoptosis resistanceof T_(CM). Importantly, eradication of HIV required elimination of theseapoptosis resistant cells if they harbor the virus.

The results were consistent with other gene expression data (GSE61697,Gene Expression Omnibus) showing higher expression of BCL-2 and lowerexpression of four other genes that impact T cell survival (TNFRSF9,TNFRSF11A, PRF1 and GZMA) in T_(CM) compared to T_(EM) (FIG. 2I;Takeshita et al., Clin. Immunol., 159:107-117 (2015)).

In light of results showing that Casp8p41 can act like a BH3-onlyprotein, there are two possible reasons why T_(CM) that reactivate HIVmight not die: Either Casp8p41 is not generated, or the proapoptoticeffects of Casp8p41 are antagonized by intrinsic resistance mechanisms.Since T_(CM) express Caspase 8 (FIG. 2E) and flow cytometry readilydetected Casp8p41 in T_(CM) from HIV-infected patients (FIG. 2F),whether there is a block to Casp8p41-mediated apoptosis was assessed.Because the Bcl-2:Caspase8 ratio is higher in T_(CM) than T_(EM) (FIG.2E), the impact of Bcl-2 on Casp8p41-mediated killing was assessed inJurkat T cells. After transfection with EGFP-Casp8p41, successfullytransfected cells were identified by their EGFP fluorescence and assayedfor cell killing using terminal deoxynucleotidyltransferase dUTP nickend labeling (TUNEL). Bcl-2 overexpression diminished the number ofEGFP-Casp8p41⁺ cells that were TUNEL⁺ (FIG. 3A, p=0.004) despite similarCasp8p41 expression (FIGS. 3B and 4). If Bcl-2 overexpressing cells dieless following HIV infection, then more cells should survive to producemore progeny HIV virions. Consistent with this prediction, Bcl-2overexpression increased cell survival following HIV infection, cellassociated HIV DNA, and HIV p24 production (FIGS. 3C-E and 5),demonstrating that altering Bcl-2 fundamentally impacts the magnitude ofviral replication and number of HIV-infected cells.

In addition, since T_(CM) express detectable levels of Caspase 8 (FIG.2E), T_(CM) from five chronically HIV-infected people were analyzed todetermine whether they generate Casp8p41 in vivo (FIGS. 2G and 2H). Flowcytometry readily detected Casp8p41 in 0.006 to 1.86% of T_(CM), as wellas 0 to 0.36% of TN and 0.006 to 1.22% of T_(EM); but was not detectedin CD3 negative cells. This frequency of Casp8p41 positivity in restingmemory CD4 T cells was similar to the frequency of Gag sequences inmemory CD4 T cells found in another study that detected 100 to 10,000Gag copies per 10⁵ highly purified sorted memory CD4 T cells from HIVinfected patients (Brenchley et al., J. Virol., 78:1160-1168 (2004)).

BCL-2 Inhibits Casp8p41-Induced Cell Death

To assess whether BCL-2 alters the ability of Casp8p41 to kill cells,the responses of parental Jurkat T cells versus Jurkat cells stablyoverexpressing BCL-2 (Jurkat-BCL-2) were compared to transientGFP-Casp8p41 expression. After transfection, Casp8p41-induced apoptosis,as measured by TUNEL positivity (FIGS. 3G and 3A), was greater inparental Jurkat cells than Jurkat-BCL-2 cells (Mean AUC 1500 vs 870 [95%CI of difference −790, −480; P=0.004]) despite similar Casp8p41expression (FIG. 3B). Thus, cells overexpressing BCL-2 die less inresponse to Casp8p41, indicating that BCL-2 antagonizes Casp8p41 inducedkilling.

To determine whether BCL-2 overexpression impacts Casp8p41-mediated BAKactivation, Jurkat or Jurkat-BCL-2 cells were transfected with GFP orGFP-Casp8p41 and stained with conformational specific antibodies thatrecognize activated BAK, but not inactive BAK. As expected,GFP-Casp8p41⁺ expressing parental Jurkat cells (identified as GFP⁺ byflow cytometry) contained more activated BAK than parental cellsexpressing GFP alone (MFI difference 52±16, P=0.029; FIGS. 3H and 3E).In contrast, GFP-Casp8p41⁺ Jurkat-BCL-2 cells did not exhibit increasedBAK activation compared to GFP alone (MFI difference 3.5±16, P=0.834),indicating that BCL-2 prevents BAK activation in response to Casp8p41expression. Accordingly, the overall number of activated BAK⁺ cellsafter GFP-Casp8p41 transfection was lower in Jurkat-BCL-2 cells comparedto Jurkat cells (P=0.045). Thus, BCL-2 inhibited Casp8p41-induced BAKactivation.

Because Casp8p41 contains an alpha helical activator domain that canbind the BH3 binding groove of Bak (Sainski et al., J. Cell. Biol.,207:159 (2014)), whether the same domain can bind antiapoptotic Bcl-2family members as well was evaluated. In initial experiments, Bcl-2 wasimmunoprecipitated from lysates of 293T cells transfected with emptyvector, HA-Casp8p41, or HA-Casp8p41 Val150Glu/Leu157KLys (a variant withdecreased affinity for Bak (Sainski et al., J. Cell. Biol., 207:159(2014))). An interaction of Bcl-2 with HA Casp8p41 that was reduced bythe Val150Glu/Leu157KLys modification was observed (FIG. 1A). In furtherexperiments, SPR demonstrated equilibrium mean dissociation constants(Kds) of 13 nM for Casp8p41 binding to purified recombinant Bcl-2, 11 nMfor Bcl-xL, and 8 nM for Mcl-1 (FIG. 1B-C). Purified activator domainpeptide also bound Bcl-2, providing evidence that the same Casp8p41domain is responsible for binding both Bak and Bcl-2 (FIG. 6). Usingmultiple low-mass molecular dynamic simulations (Pang, Biochem. Biophys.Res. Commun., 452:588-592 (2014)), a three-dimensional model of thatpeptide bound in the BH3 binding groove of Bcl-2 (FIG. 1D) that predictsa critical interaction of Bcl-2 Arg146 with Casp8p41 Glu147 and Glu154was determined. Substitution of Ala for Bcl-2 Arg146, which inhibitsBcl-2.Bim interaction (Smith et al., J. Biol. Chem., 286:17682-17692(2011)), decreased the affinity of Bcl-2 for the Casp8p41 activatorpeptide (FIG. 6) or full length Casp8p41 250-fold (FIG. 1E-F),confirming that Casp8p41 binds the Bcl-2 BH3 binding groove. The modelalso predicted that Casp8p41 Val150 and Leu157 bind in the twohydrophobic regions in the Bcl-2 BH3 binding groove. Consistent withthis prediction, the affinity of Casp8p41 for Bcl-2 was reduced over300-fold by the Val150Glu/Leu157Lys Casp8p41 modification (FIG. 1G-H).These results indicate that the Casp8p41 activator domain can interactwith the BH3 binding groove of anti-apoptotic Bcl-2 family members aswell as Bak.

Venetoclax is a Clinically Relevant BCL-2 Antagonist that ImpactsCasp8p41-Mediated Killing

Venetoclax (formerly known as ABT-199), potently and selectivelyinhibits BCL-2 binding to BH3 domains (Souers et al., Nat. Med.,19:202-208 (2013)), is well tolerated in early phase clinical trials(Correia et al., Biochim Biophys Acta, 1853:1658-1671 (2015)), andachieves peak plasma levels of up to 5 μM (Matthew et al., Blood,122:872 (2013)). The impact of venetoclax on T cells expressing Casp8p41or reactivating HIV was assessed. In initial experiments, treatment withincreasing doses of venetoclax (up to 1 μM) did not result in increasedapoptosis of either parental Jurkat cells transfected with no DNA orJurkat cells expressing eGFP compared to diluent control (FIG. 11A). Incontrast, venetoclax (1 μM) significantly increased cell death in Jurkatcells expressing eGFP-Casp8p41 (mean difference 25.7±10.3%, P=0.016,FIG. 11A). This selective enhancement of killing induced by Casp8p41 butnot generalized toxicity was further evaluated by treating primaryuninfected CD4 T cells with venetoclax. Importantly, uninfected CD4 Tcells (N=7 patients) treated with venetoclax (1 μM) for up to five daysdid not exhibit reduced viability compared to control treated cells(mean difference −7.2±4.8% at Day 5, P=0.16, FIG. 11B). Furthermore,uninfected CD4 T cells treated with venetoclax did not exhibit alteredmitogen-induced proliferation as measured by CFSE dilution (meandifference in percent CFSE low cells at Day 3 −1.1±7.9%, P=0.90, FIG.11C). The lack of toxicity of venetoclax towards CD4 T cells from HIVuninfected donors was also seen using cells from HIV infected, but ARTsuppressed, patients; venetoclax (1 μM) for 24 hours did not adverselyaffect viability of bulk primary CD4 T cells (mean difference −4.7±1.6%viable, FIG. 11D). These favorable safety findings in vitro have alsobeen seen in vivo: in 40 NHL patients receiving venetoclax monotherapy,only 2 cases of dose limiting neutropenia were observed (Matthew et al.,J. Clin. Oncol., 32:53 (2014)). These results demonstrate thepossibility that venetoclax can be used safely in HIV infected patients.

Simultaneous Detection of Markers of HIV Infection and Apoptosis

If BCL-2 neutralizes Casp8p41, then antagonizing BCL-2 should augmentCasp8p41-induced killing, including when Casp8p41 is generated bylatently HIV infected cells that reactivate the virus. Before testingthis possibility, whether select markers (protein or nucleic acid based)remain detectable was first assessed when the cell of interest isundergoing death. Jurkat T cells stably expressing eGFP were treatedwith vehicle control or the cytotoxic quinolone alkaloid CPT to induceapoptosis, then examined for expression of eGFP (as a prototypiccytoplasmic protein) and actin mRNA (as a prototypic mRNA) over time.Treatment of GFP+ Jurkat cells with CPT decreased cell viability asmeasured by cellular ATP content (FIG. 12A) and light scatter (FIG. 12B)compared to diluent-treated cells.

Coincident with the loss in viability was a decrease in detectable eGFP(17% eGFP+ with CPT vs. 91% eGFP+ with diluent, FIG. 12C) and detectableactin message (34% reduction compared to diluent control) as assessed byqRT-PCR (FIG. 12D). As the proportion of active caspase-3⁺ cells (FIG.12E), TUNEL+ cells (FIG. 12F) or membrane permeable cells (FIG. 12G)increased over time, there was a reciprocal decrease in detectable eGFP(FIG. 12C) despite the fact that virtually all cells were eGFP positiveat baseline. For example, by 48 hours, 97% of CPT treated cells wereeGFP negative, despite having been uniformly eGFP positive. Accordingly,estimating the proportion of dead or dying cells that express adegradable marker of interest (e.g., HIV p24 or HIV RNA/DNA) willsubstantially underestimate the proportion of cells that expressed themarker before encountering the death stimulus. Therefore, the ability todetect protein or nucleic acid based phenotypic markers is impaired ascell death proceeds, rendering this approach insensitive and prone toincorrect phenotyping of the dying cell.

Accordingly, to approach the question of whether HIV reactivation inconcert with BCL-2 antagonism reduces cell associated HIV DNA, wecompared HIV DNA content in treated compared to control samples ratherthan simultaneously assessing markers of HIV and cell death in the samecells.

Again, if Bcl-2 inhibits HIV induced cell death by binding the Casp8p41activator domain, disruption of this interaction should augment bothCasp8p41-mediated killing and HIV-induced cell death. Consistent withthis possibility, the Bcl-2 antagonist ABT-19914 increased killing byEGFP-Casp8p41 (FIGS. 7A and 8), but not control vector. Likewise,ABT-199 decreased survival of CD4 T cells following acute HIVIIIbinfection (FIGS. 7B and 9), but had no effect on survival ormitogen-induced proliferation of mock-infected CD4 T cells (FIG. 7B-C).In addition, ABT-199 reduced supernatant HIV p24 levels (FIG. 7D),potentially reflecting death of HIV producing cells, a direct effect ofABT-199 on HIV replication, or both. Indeed, HIV LTR-Luciferase reporterconstructs demonstrated that ABT-199 inhibits both basal andprostratin-induced HIV transcription in primary CD4 T cells (FIG. 7E).While the mechanism by which ABT-199 inhibits HIV LTR transcription isunknown, Bcl-2 overexpression has been associated with NFκB activationin some studies (Mortenson et al., J. Cell. Biochem., 102:1171-1179(2007)), but not others (Grimm et al., J. Cell Biol., 134:13-23 (1996)).ABT-199 also decreased cell associated HIV-1 DNA compared to vehiclecontrol treated cells (FIG. 7F). These results, coupled with the lack oftoxicity of ABT-199 in uninfected cells (FIG. 7B), demonstrate thatABT-199 preferentially kills HIV-infected cells, resulting in lower HIVreplication and fewer HIV infected cells. Similar effects on survival ofinfected cells, p24 production, and cell-associated HIV-1 DNA were seenwith navitoclax (FIG. 7G-I), an inhibitor of Bcl-2, Bcl-xL, and Bcl-w(Tse et al., Cancer Res., 68:3421-3428 (2008)), although navitoclaxcaused more toxicity in uninfected cells (FIG. 7G).

Because ABT-199 reduces HIV replication and decreases the number ofcells containing HIV DNA during acute infection in vitro, the effects ofthis agent during HIV latency were examined. When cryopreserved CD4 Tcells from suppressed HIV-infected patients were purified, treated withdiluent or ABT-199, and reactivated with αCD3/αCD28 in the presence oftenofovir and raltegravir to prevent spreading infection, ABT-199reduced cell associated HIV DNA in a dose dependent manner (FIG. 10A).In addition, 8 of 11 (73%) freshly isolated primary CD4 T cell sampleswith cell associated HIV DNA measurable in the control sample exhibiteda decrease after ABT-199 (FIG. 10B). ABT-199 also increased theproportion of Casp8p41 positive T_(CM) cells containing active caspase 3(FIG. 10C), indicating that Bcl-2 inhibition enhances Casp8p41-mediatedkilling of HIV-infected T_(CM) cells that reactivate HIV.

Active caspase 3 (a marker of apoptotic cell death) was assessed in p24+(HIV infected) and p24− cells that were primed with venetoclax andreactivated with αCD3/αCD28. Median cell death, as measured by activecaspase 3 staining in the p24− cells, was 2.5% in the control treatedαCD3/αCD28 sample and was not changed significantly by venetoclax(10.3%, P=0.189, FIG. 10D). In contrast, venetoclax increased theproportion of HIV p24+CD4+ cells that are active caspase 3+ compared tocontrol treated cells (from 23% active caspase 3+ in control sample to47% active caspase 3+ in the venetoclax sample, P=0.026, FIG. 10D). Ofnote, the frequency of p24 positive cells in reactivated CD4 T cells wassimilar to other previous reports (Deng et al., Nature, 517:381-385(2015); and Pegu et al., Nat. Commun., 6:8447 (2015)). HIV RNA in thecell culture supernatant was not altered by venetoclax treatmentcompared to control (FIG. 10E), indicating that venetoclax does notimpair the ability of cells to reactivate HIV.

The results provided herein demonstrate that Casp8p41 interacts withantiapoptotic Bcl-2 family members. Conversely, Bcl-2 inhibitionreleased Casp8p41 and pro-apoptotic Bcl-2 family members, causing moreHIV infected cells to die and thereby resulting in reduced HIVreplication and fewer cells that contain HIV DNA. Importantly, the HIVreservoir was reported to be stable over time (Josefsson et al., Proc.Natl. Acad. Sci. USA, 110:E4987-4996 (2013)) and unaffected byantiretroviral therapy intensification (Puertas et al., AIDS, 28:325-334(2014) even in conjunction with therapeutic vaccination (Achenbach etal., The Lancet HIV, 2:e82-e91 (2015)). In contrast, the resultsprovided herein demonstrate that a single treatment with ABT-199 can,through release of Casp8p41, diminish HIV DNA, providing the firstevidence that it is possible to pharmacologically diminish HIV reservoirsize.

In summary, these results demonstrate that venetoclax-mediatedinhibition of BCL-2 in all cells has minimal effect on cell viability inuninfected cells (FIG. 11) yet promotes the preferential killing ofp24+459 (HIV replicating) cells. Moreover, these results demonstrate theidentification of a clinically relevant treatment that converts HIVreactivation from latency without killing of the reactivating cell (FIG.13A) into an event that kills the reactivating cell by priming all cellstowards apoptosis sensitive phenotype and then allows HIV infectedcells, which replicate virus and generate Casp8p41, to undergo apoptosiswhen BCL-2 is inhibited (FIG. 13B).

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

1. A method for killing HIV infected cells within a human infected withHIV, wherein said method comprises: (a) administering a Bcl-2 inhibitorto said human, and (b) administering a latency reversing agent to saidhuman.
 2. The method of claim 1, wherein said cells are CD4⁺ T cells. 3.The method of claim 1, wherein said Bcl-2 inhibitor is ABT-199.
 4. Themethod of claim 1, wherein said latency reversing agent is selected fromthe group consisting of an HDAC inhibitor, a phorbol ester, IL-2, and abromodomain inhibitor.